[yucca]

Since you are coming the PC-side of things, why not post the apps you were using to do these things before? It might shake some better ideas loose . . .

OO is a super outliner and light database - I own it and use it all the time.

OF is a personal task manager with a strong GTD bias, and may do for your project planning provided you don't need to track the work of others with it (in which case you might want to look at OmniPlan). Like OO, it is outline/hierarcy based; and is not great for many-to-many "interconnections". I suggest you checkout the intro video if you haven't done so already.

With that out of the way, it looks like you need a reference collection and organization tool. That is something that neither OO nor OF is really designed to do. Yojimo (Bare Bones Software) or NoteBook (Circus Ponies) seem like good fits for your needs.